Frequently asked questions about GEOS-Chem: Difference between revisions

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On this page we shall answer some commonly asked questions about GEOS-Chem.
On this page we shall answer some commonly asked questions about GEOS-Chem.


== Basic information about GEOS-Chem ==
== For new users ==


=== For new users ===
* [https://geos-chem.seas.harvard.edu/welcome.html I am a GEOS-Chem new user.  What is expected of me?]
 
* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/related-docs.html Where can I find user manuals for GEOS-Chem and related software?]
* [[GEOS-Chem welcome letter for new users|I am a GEOS-Chem new user.  What is expected of me?]]
* [[Minimum system requirements for GEOS-Chem|On what types of machines can I run GEOS-Chem?]]
* [http://cloud.geos-chem.org Can I use GEOS-Chem on cloud-computing platforms?]
* [http://cloud.geos-chem.org Can I use GEOS-Chem on cloud-computing platforms?]
* [[Species in GEOS-Chem|What types of simulations can I run with GEOS-Chem?]]
* [[Guide to GEOS-Chem simulations|What types of simulations can I run with GEOS-Chem?]]
* What is the [[GEOS-Chem horizontal grids|horizontal resolution]] and [[GEOS-Chem vertical grids|vertical resolution]] of GEOS-Chem?
* What is the [[GEOS-Chem horizontal grids|horizontal resolution]] and [[GEOS-Chem vertical grids|vertical resolution]] of GEOS-Chem?
* [[Overview of GMAO met data products|Which meteorological data fields can be used by GEOS-Chem?]]
* [[Overview of GMAO met data products|Which meteorological data fields can be used by GEOS-Chem?]]
* [[Submitting GEOS-Chem support requests|To whom can I direct GEOS-Chem-related questions?]]
* [https://geos-chem.readthedocs.io/en/latest/help-and-reference/SUPPORT.html To whom may I direct GEOS-Chem-related questions?]
* [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html What does the GEOS-Chem Steering Committee do?]
* [https://geoschem.github.io/steering-cmte.html What does the GEOS-Chem Steering Committee do?]
* [http://acmg.seas.harvard.edu/geos/geos_working_groups.html What do the GEOS-Chem Working Groups do?]
* [https://geoschem.github.io/working-groups.html What do the GEOS-Chem Working Groups do?]
* [[GEOS-Chem Support Team|What does the GEOS-Chem Support Team do?]]
* [https://geoschem.github.io/support-team What does the GEOS-Chem Support Team do?]
* [[Subscribing_to_the_GEOS-Chem_email_lists|I see that there are several GEOS-Chem email lists.  How can I subscribe?]]
* [https://geoschem.github.io/email-lists I see that there are several GEOS-Chem email lists.  How can I subscribe?]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
== Science questions ==
 
=== Science questions ===


Where can I find information about ...
Where can I find information about ...


* [[GEOS-Chem chemistry mechanisms|the available chemical mechanisms in GEOS-Chem?]]
* [[Guide to GEOS-Chem simulations|types of GEOS-Chem simulations that I can run?]]
* [[Bromine chemistry mechanism|the bromine chemistry mechanism in GEOS-Chem?]]
* [[Bromine chemistry mechanism|bromine chemistry?]]
* [[FlexChem|the KPP chemical solver?]]
* [https://kpp.readthedocs.io The chemical solver used in GEOS-Chem?]
* [[Linoz stratospheric ozone chemistry|the Linoz stratospheric ozone chemistry scheme?]]
* [[Linoz stratospheric ozone chemistry|the Linoz stratospheric ozone chemistry scheme?]]
* [[GEOS-Chem_chemistry_mechanisms#Stratospheric_chemistry|the stratospheric chemistry mechanism?]]
* [[Offline chemistry simulations|Other chemistry simulations such as CO2, CH4, Hg, etc.?]]
* [[HEMCO data directories|emissions options in GEOS-Chem?]]
* [[Advection scheme TPCORE|the advection scheme in GEOS-Chem?]]
* [[Advection scheme TPCORE|the advection scheme in GEOS-Chem?]]
* [[Boundary layer mixing|the boundary layer mixing schemes in GEOS-Chem?]]
* [[Boundary layer mixing|the boundary layer mixing schemes in GEOS-Chem?]]
* [[Cloud convection|the cloud convection schemes in GEOS-Chem?]]
* [[Cloud convection|the cloud convection schemes in GEOS-Chem?]]
* The [[Dry deposition]] and [[Wet deposition]] schemes in GEOS-Chem?
* The [[Dry deposition]] and [[Wet deposition]] schemes in GEOS-Chem?
* [[GEOS-Chem nested grid simulations]]?
* [https://geos-chem.readthedocs.io/en/latest/supplemental-guides/nested-grid-guide.html GEOS-Chem nested grid simulations]?


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
== Technical issues ==


=== Technical issues ===
* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/get-code.html How do I download the GEOS-Chem source code]
* [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/create-rundir.html How do I create run directories?]
* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/error-guide.html What should I do when I encounter an error while running GEOS-Chem]?
* [https://github.com/geoschem/geos-chem/issues Is there a comprehensive list of GEOS-Chem bug reports?]
* Do you have any information on how I can [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/debug-guide.html debug GEOS-Chem or HEMCO errors]?


* [[Using Git with GEOS-Chem#Downloading a new GEOS-Chem version|How do I download the GEOS-Chem source code and run directories?]]
== Parallelization issues ==
* [[Common GEOS-Chem error messages|What should I do when I encounter an error while running GEOS-Chem]]?
* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/parallel-guide.html#how-can-i-tell-what-should-go-into-the-omp-private-clause How can I tell if a variable has to be declared with <tt>!$OMP PRIVATE</tt> or <tt>!$OMP SHARED?</tt>]
* Do you have any information about [[GEOS-Chem performance]] and [[GEOS-Chem_performance#GEOS-Chem_scalability|GEOS-Chem Scalability]]?
* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/parallel-guide.html#how-many-cores-may-i-use-for-geos-chem-or-hemco How many CPU cores may I use for my GEOS-Chem Classic simulation?]
* [[GEOS-Chem Makefile Structure|Where can I learn more about the GEOS-Chem Makefiles?]]
* [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/parallel-guide.html#why-is-geos-chem-is-not-using-all-the-cores-i-requested Why is GEOS-Chem Classic not using all the CPU cores that I requested?]
* [[Bugs and fixes|Is there a comprehensive list of GEOS-Chem bugs and how they were fixed?]]
* [[GEOS-Chem basics|I am new to programming. Do you have any online resources or tutorials?]]
* Are there any [[Floating point math issues|numerical issues]] that I should be aware of?
* Do you have any tools that would help me [[Debugging with the GEOS-Chem unit tester|debug GEOS-Chem more efficiently?]]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
== High-Performance GEOS-Chem (GCHP) ==


=== Parallelization issues ===
Please see the GCHP user manual at [https://gchp.readthedocs.io <tt>gchp.readthedocs.io</tt>]for more information.
* [[Parallelizing_GEOS-Chem#How_can_I_tell_if_a_variable_has_to_be_declared_with_PRIVATE_or_SHARED.3F|How can I tell if a variable has to be declared with <tt>!$OMP PRIVATE</tt> or <tt>!$OMP SHARED?</tt>]]
* [[Parallelizing_GEOS-Chem#How_many_CPUs_may_I_use_in_my_GEOS-Chem_simulation.3F|How many CPUs may I use for my GEOS-Chem simulation?]]
* [[Parallelizing_GEOS-Chem#Why_is_GEOS-Chem_is_not_using_all_the_CPUs_I_requested.3F|Why is GEOS-Chem not using all the CPUs that I requested?]]
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:45, 2 January 2019 (UTC)
 
=== High-Performance GEOS-Chem (GCHP) ===
 
Please see the [[GCHP_Main_Page|GCHP main wiki page]] for information about GCHP.


== Where can I get restart files for GEOS-Chem? ==
== Where can I get restart files for GEOS-Chem? ==


For instructions on how to obtain a set of sample restart files that you can use to spin up your own simulations, please see [[GEOS-Chem_basics#Restart_files|the ''Restart Files'' section of our ''GEOS-Chem basics'' wiki page]].
For instructions on how to obtain a set of sample restart files that you can use to spin up your own simulations, [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/restart-files-gc.html#where-can-i-get-a-restart-file-for-my-simulation please visit this link].
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:24, 6 January 2017 (UTC)


== Running GEOS-Chem ==
== Running GEOS-Chem ==


Please see our ''[[Running GEOS-Chem]]'' wiki page.
Please see the [https://geos-chem.readthedocs.io/en/latest/gcclassic-user-guide/run.html Run your simulation] section of [https://geos-chem.readthedocs.io <tt>geos-chem.readthedocs.io.</tt>]. for more information.
 
=== How long does GEOS-Chem take to run? ===
 
It depends on your particular computing environment.  We have posted several timing results from GEOS-Chem [[GEOS-Chem_performance#7-day_time_tests|7-day time test simulations]].
 
=== GEOS-Chem seems to be running too slowly.  What can I do? ===
 
You should be aware of [[GEOS-Chem Makefile Structure#Compile-time options that can slow down GEOS-Chem|several compile-time options that will slow down GEOS-Chem]].  Use these options only for debugging, but not in your production runs.
 
If you are archiving many diagnostic quantities are a high temporal resolution (e.g. every hour), then this will increase the run time of your simulation.  You can try saving out less diagnostic quantities, or archiving at a lower temporal resolution (e.g. every day).
 
== GEOS-Chem errors ==
 
Please also see our ''[[Guide to GEOS-Chem error messages]]''.
 
=== GEOS-Chem died with an error.  What can I do? ===
 
First, you should try to understand the type of error that has occurred.  There are several different classes of errors, such as:
 
# [[Common GEOS-Chem error messages#File_I.2FO_errors|File I/O errors]]
#* Errors caused by incorrect input options
#* Errors caused by missing data files
#* Errors caused by corrupted data files
#* [[Common GEOS-Chem error messages#Error computing F_OF_PBL|Running GEOS-Chem at the wrong resolution for the data files]]
# [[Common GEOS-Chem error messages#Crashes or abnormal exits|Abnormal exits]]
#* From the [[KPP solvers FAQ|KPP chemical solver]]
#* From other areas of GEOS-Chem
# [[Common GEOS-Chem error messages#General types of errors|Technical errors]]
#* [[Common GEOS-Chem error messages#Segmentation faults|Segmentation faults]]
#* [[Common_GEOS-Chem_error_messages#Array-out-of-bounds_error|Array-out-of-bounds errors]]
#* Out of memory errors
 
Once you have understood the type of GEOS-Chem error that has occurred, you can take steps to fix it. In some cases, the fixes will be simple (i.e. selecting the proper option and starting over, or replacing missing or corrupted data files, etc.).  In other cases, the error may be more difficult to diagnose (such as a [[KPP_solvers_FAQ#How_do_I_choose_the_absolute_and_relative_tolerance.3F|convergence error in the chemical solver]]).  In that case you may have to "dig in" to the code so that you can modify its behavior (e.g. modify convergence criteria, add error checks, etc.).
 
Try to isolate the error to a particular GEOS-Chem routine.  You can use a debugger such as idb or Totalview, or you can turn on the ND70 debug printout option.  (ND70 will print debug messages to the log file after key operations have been completed.)  You may also try turning off operations (e.g. wet deposition, dry deposition, chemistry) one at a time in the <tt>input.geos</tt> file to isolate the error. Once you know where the error is occurring, try to print out values for a given grid box and tracer, either in the debugger or by adding PRINT statements to the code. You will gain great insight into what is happening by using this technique.
 
Try to determine if the error is persistent (i.e. if it always occurs at the same model time/date or if it occurs at different times and dates in the simulation).  A persistent error could indicate a missing or corrupted data file, or a flaw in the scientific algorithm being used.  Non-persistent errors (i.e. those that don't happen at the same model time and date) may indicate memory errors, such as array-out-of-bounds, segmentation faults, or that the code is using more memory than is available.
 
If you still cannot determine the error from the traceback output, recompile with the <tt>BOUNDS=yes</tt> compiler option. This will check to see if an array is being accessed incorrectly
 
Please see our ''[[Guide to GEOS-Chem error messages]]'', which contains strategies for recognizing and fixing several commonly-encountered error conditions.  If you still cannot determine the source of your error, please [[Submitting GEOS-Chem support requests|contact the GEOS-Chem Support Team for assistance]].
 
=== Where does GEOS-Chem error output get printed? ===
 
GEOS-Chem, like all Unix programs, sends its output to two streams:
 
# stdout
# stderr
 
==== The stdout stream ====
 
Most GEOS-Chem output will go to the '''stdout''' stream, which takes I/O from the Fortran WRITE and PRINT commands.  If you run GEOS-Chem by just typing the executable name at the Unix prompt:
 
geos
 
then the stdout stream will be printed to the terminal window.  You can also redirect the stdout stream to a log file with the Unix redirect command:
 
geos > log
 
We recommend that you create GEOS-Chem log files so that you can reexamine the output from your run at a later time.
 
Most GEOS-Chem errors will be printed to stdout (and hence, to the log file). Most errors flagged by GEOS-Chem use a standard error message format, such as:
 
==============================================================
GEOS-CHEM ERROR: No output scheduled on last day of run!
STOP at IS_LAST_DAY_GOOD ("input_mod.f")
==============================================================
 
==== The stderr stream ====
 
The '''stderr''' stream takes I/O from various Unix system commands, including <tt>exit</tt>.  If your GEOS-Chem run died as a result of a system problem (i.e. you ran up against a system time or memory limit, you are over disk quota, etc.), then the error message will more than likely go to stderr instead of stdout.  As a result, these error messages will not be printed to the GEOS-Chem log file output.
 
If you use a queue system then the stderr output may be printed to a file. For example, if you submit a GEOS-Chem job to the SGE queue system, and your job script is named <tt>run.geos</tt>, SGE will send the stderr output to a file named <tt>run.geos.oXXXXX</tt> (where XXXXX is the job ID #).


--[[User:Bmy|Bob Y.]] 15:44, 8 November 2010 (EST)
There are several ways to [https://geos-chem.readthedocs.io/en/latest/gcc-guide/05-run/run-speedup.html speed up a slow GEOS-Chem simulation].  If you are archiving many diagnostic quantities are a high temporal resolution (e.g. every hour), then this will increase the run time of your simulation.  You can try saving out less diagnostic quantities, or archiving at a lower temporal resolution (e.g. every day).

Latest revision as of 17:02, 23 May 2024

On this page we shall answer some commonly asked questions about GEOS-Chem.

For new users

Science questions

Where can I find information about ...

Technical issues

Parallelization issues

High-Performance GEOS-Chem (GCHP)

Please see the GCHP user manual at gchp.readthedocs.iofor more information.

Where can I get restart files for GEOS-Chem?

For instructions on how to obtain a set of sample restart files that you can use to spin up your own simulations, please visit this link.

Running GEOS-Chem

Please see the Run your simulation section of geos-chem.readthedocs.io.. for more information.

There are several ways to speed up a slow GEOS-Chem simulation. If you are archiving many diagnostic quantities are a high temporal resolution (e.g. every hour), then this will increase the run time of your simulation. You can try saving out less diagnostic quantities, or archiving at a lower temporal resolution (e.g. every day).

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